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<title>Basic DB Hits Query</title>
<h1>Basic DB Hits Query</h1>

This query allows you to "build" a table
of results from multiple queries, which can be Copied to Clipboard, 
Exported, or view the individual HitIDs (or SeqIDs) with "View Selected Hit". 
<p>
Search by substring: There is a table associated with each of the search modes (Hit ID, and Description);
if you switch search modes, you switch tables.
<ul>
<li><b>Hit IDs:</b> Identifier of the hit, e.g. UniProt ID
<li><b>Descriptions:</b> Hit description, e.g. UniProt description string
</ul>
Search by other features:
<ul>
<li><b>AnnoDBs:</b> Show results from one or more annotation databases <sup>1</sup>
<li><b>Species:</b> Show results from one or more species<sup>2</sup>
<li><b>Attributes:</b> Several additional hit filters such as BLAST E-value, Rank, KEGG ID, etc. <sup>3</sup>
</ul>
<p>Select one or more filters to query on, then press "Add to table" to execute the 
search. 
<br>Columns can be added/removed ("Select Columns"), 
rearranged by dragging and sorted. 

<p><b>Group by Hit ID:</b>
<ul>
<li>If this option is selected, then the table has one entry for each annotation (i.e. hit ID), 
showing the number of sequences hit by that annotation, and the sum of count data for all of those 
sequences. Selecting a Hit ID followed by "View Selected Hit" will
show all sequences with the Hit ID in the main table.
<li>If unselected, then the table shows each SeqID/HitID pair as a separate line. 
<li>This is applied to the contents of the table, so can be applied <i>after</i> a search.
</ul>


<p><b>Buttons at bottom of table:</b> 
<ul>
<li>Delete all: deletes everything in the table. If you do not want to append 
the results of a query to the existing results, you will need to specifically
delete the existing results.
<li>Unselect: if you have a sequence selected, this will unselect it.
<li>Delete selected: delete the selected sequence from the table.
<li>Keep selected: delete everything except the selected.
</ul>
You can select multiple sequences by holding down the 'shift' or 'ctrl' keys while selecting sequences.
<hr>
<sup>1</sup><b>AnnoDB</b>: The sequences are annotated against one or more annotation databases.
Only hits from the selected databases will be shown.

<p><sup>2</sup><b>Species</b> The species of the annotation is read from the description
line in the fasta annotation file (if available). Only hits from the selected species will
be shown.

<p><sup>3</sup><b>Attributes</b>
<ul>
<li>Best Anno Hit: the best evalue hit that has an informative description, i.e. does not
contain phrases such as "uncharacterized protein".
<li>Rank: a rank is assigned to each hit based on its order in the BLAST file, which are ordered
by e-value (so the smaller ranks are the smaller evalues). 
<li>KEGG, PFam, and EC will only be available if UniProt database(s) were used for annotation
and the .dat file was available. 
<ol>
<li>If KEGG is checked and no string is entered, all hits that have a KEGG will be shown.
<li>If a substring is entered, KEGG must be checked; all hits with the substring in the KEGG ID will be shown.
<li>The same two rules apply to EC and PFam.
</ol>
</ul>
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